Things I will do:
I turn off mobGriefing because I'm more of a builder than anything else. It would suck to have a matterfab destroyed by a creeper, but to me it's much worse if an enderman sticks a random dirt block in my base. I've never actually had a creeper blow up in a base I've made, but even if one did fixing the damage would likely be more annoyance than actual gameplay.
Similarly, I do most of my building on peaceful. It takes a long time to build some of my structures, so I don't want to waste time running back to my bed to switch to day.
I turn off fire spread. Again, I'm a builder at heart. I'm not gonna let a stray lightning bolt burn down one of my creations. However, I might consider turning this back on in my current world if I make a lightning rod or start doing a lot of reckless thaumcrafting since the lightning danger is a balancing point.
I toggle rain off all the time because it can just be annoying. No gameplay reason, just a matter of whether I want to avoid hearing it.
I have occasionally changed the time to night if I would have afked waiting for it to come around anyway. For example, I've changed time to night so I could hunt endermen when I was waiting on ender pearls to continue my project. I would probably act similarly switching things to day, but that's what beds are for.
I revert the Matterfab EU requirement to the standard IC2 amount while playing SSP. IMO, the energy requirement for the Matterfab is balanced around a server running 24/7. For SSP I just don't see how it makes sense. However, I don't re-enable the Massfab. All that iridium-based stuff should still take a while to get, so I don't mind having to wait a while to start on the production of UU.
I once spawned in a stack of feathers to expedite Thaumcraft research. I already had an automatic chicken farm up and running, but I didn't want to wait for more feathers so I spawned them in and deleted a stack from the farm later.
I've switched to creative mode a few times to fly back to my batbox when my jetpack ran out of juice rather than nerd poling my way up.
Things I won't do:
Nether lava. It's just too easy for my tastes. I'll do netherrack in a magma crucible, but only for limited lava production. For things like lava centrifuging I either use overworld lava or cobble in a magma crucible. I'm also looking into supplying lava via bees.
Soul Shard + Anvil exploit/bug. I've been tempted to use it a few times to get some of the more ridiculous shards, but I found it much more interesting to devise systems that works around those limitations.
Power systems reliant on solar. I don't mind mixing in a panel or 2 - they're great for low-power operations with 100% uptime like my AE network, but they're just not very interesting. I don't really consider them cheating, I just don't use them beyond supplemental power.
Revert GT recipe changes. I totally get why people hate a lot of these, but I've played with mods for so long that I really appreciate how building things the GT way can incorporate so many mods. Even if you have to use different power systems for some of the parts, it makes for a more unified experience imo. The one quibble I have is the macerator. Sometimes I revert that to easy mode, other times I change the pulverizer to hard mode. It doesn't make any sense to have one easy and one hard, though.
Mindlessly copy ComputerCraft programs. This one is a bit fuzzy because I've definitely changed my views on the issue over time. A first I had no clue how to code, so I just used programs I found online. As I learned a bit of LUA I made tweaks to some of those programs and wrote some simple ones for myself. In my current world I only use programs that I either coded myself or tweaked to suit my personal style. Giving up AustinKK's OreQuarry hurt, but turtles are already such cheap auto-miners that I didn't feel too bad.